MolNFT v1 · #168661 · protein
Structure of the rieske non-heme iron oxygenase gxta with dideoxysaxitoxin bound
6WND · Sxtdiox: “Structure of the rieske non-heme iron oxygenase gxta with dideoxysaxitoxin bound”. X-ray diffraction, 4 ligands (FES, U5A, FE), 15 pockets (best druggability 0.80). MolNFT v1 #168661 on GenesisL1: 3D structure, binding…
- PDB
- 6WND
- Type
- protein
- Length
- 955 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sxtdiox
- UniProt
- C3RVP5
- Ligands
- FES, U5A, FE, CL
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sxtdiox | protein | 311 | 23% helix, 33% strand | C3RVP5 |
| B | Sxtdiox | protein | 320 | 22% helix, 34% strand | C3RVP5 |
| C | Sxtdiox | protein | 324 | 20% helix, 33% strand | C3RVP5 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- U5A · [(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, C
- GOL · Glycerol · additive · 14 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.80 | 0.86 | 53 | U5A |
| 2 | 312 | 0.78 | 0.89 | 39 | U5A |
| 3 | 372 | 0.78 | 0.87 | 44 | U5A |
| 4 | 168 | 0.58 | 0.82 | 27 | empty |
| 5 | 319 | 0.57 | 0.76 | 37 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 873 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 260 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WND · Structure of the Rieske non-heme iron oxygenase GxtA with dideoxysaxitoxin bound · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C3RVP5
- Elsewhere: RCSB PDB 6WND · PDBe 6WND · UniProt C3RVP5
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